Variant report

Variant	rs1035104
Chromosome Location	chr1:223406806-223406807
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:223406012-223407301	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr1:223406579-223407809	HCT-116	colon:	n/a	n/a
3	USF1	chr1:223406738-223407233	K562	blood:	n/a	n/a
4	MAX	chr1:223406723-223407216	SK-N-SH	brain:	n/a	n/a
5	EGR1	chr1:223406608-223407608	HCT-116	colon:	n/a	chr1:223406663-223406676
6	CTCF	chr1:223406720-223406870	AoAF	blood vessel:	n/a	n/a
7	UBTF	chr1:223406706-223407234	K562	blood:	n/a	n/a
8	MAX	chr1:223406716-223407314	SK-N-SH	brain:	n/a	n/a
9	GATA2	chr1:223406795-223407413	HUVEC	blood vessel:	n/a	chr1:223407048-223407058 chr1:223407044-223407065 chr1:223407051-223407058 chr1:223407051-223407058 chr1:223407051-223407058 chr1:223407046-223407060
10	TEAD4	chr1:223406436-223407813	K562	blood:	n/a	n/a
11	HDAC2	chr1:223406752-223407239	K562	blood:	n/a	n/a
12	POLR2A	chr1:223406806-223407292	HCT-116	colon:	n/a	n/a
13	CTCF	chr1:223406760-223406910	HCFaa	heart:	n/a	n/a
14	JUND	chr1:223406734-223407542	K562	blood:	n/a	chr1:223407081-223407090 chr1:223407468-223407477 chr1:223407285-223407297
15	ZNF143	chr1:223406740-223407125	GM12878	blood:	n/a	chr1:223406912-223406930
16	MYC	chr1:223406765-223407197	K562	blood:	n/a	n/a
17	MAX	chr1:223406450-223407024	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:223406797-223407246	HUVEC	blood vessel:	n/a	n/a
19	ARID3A	chr1:223406575-223407472	K562	blood:	n/a	chr1:223406715-223406731 chr1:223406738-223406754
20	MAFF	chr1:223406591-223407533	K562	blood:	n/a	n/a
21	E2F6	chr1:223406507-223407656	K562	blood:	n/a	n/a
22	TBL1XR1	chr1:223406435-223407498	K562	blood:	n/a	n/a
23	CTCF	chr1:223406680-223406830	HCT-116	colon:	n/a	n/a
24	EP300	chr1:223406345-223407252	GM12878	blood:	n/a	chr1:223407082-223407091 chr1:223407044-223407058
25	IKZF1	chr1:223406444-223407216	GM12878	blood:	n/a	n/a
26	CTCF	chr1:223406760-223406910	A549	lung:	n/a	n/a
27	CTCF	chr1:223406720-223406870	HAc	cerebellar:	n/a	n/a
28	CTCF	chr1:223406740-223406890	SAEC	small airway:	n/a	n/a
29	CTCF	chr1:223406740-223406890	NHEK	skin:	n/a	n/a
30	REST	chr1:223406796-223407229	K562	blood:	n/a	n/a
31	CTCF	chr1:223406800-223406855	K562	blood:	n/a	n/a
32	CBX3	chr1:223406125-223409533	K562	blood:	n/a	n/a
33	EBF1	chr1:223405803-223407445	GM12878	blood:	n/a	n/a
34	ELK1	chr1:223406755-223407081	K562	blood:	n/a	n/a
35	MXI1	chr1:223406485-223407698	IMR90	lung:	n/a	n/a
36	MYC	chr1:223406727-223407270	K562	blood:	n/a	n/a
37	MXI1	chr1:223406633-223407113	GM12878	blood:	n/a	n/a
38	USF1	chr1:223406665-223407166	K562	blood:	n/a	n/a
39	STAT5A	chr1:223406466-223407469	K562	blood:	n/a	chr1:223406994-223407008 chr1:223407381-223407389
40	HEY1	chr1:223406696-223407253	K562	blood:	n/a	n/a
41	FOSL2	chr1:223406722-223407344	SK-N-SH	brain:	n/a	chr1:223407081-223407090 chr1:223407285-223407297
42	TCF12	chr1:223406626-223407418	SK-N-SH	brain:	n/a	n/a
43	MAX	chr1:223406687-223407664	K562	blood:	n/a	n/a
44	PML	chr1:223406680-223407292	K562	blood:	n/a	n/a
45	E2F4	chr1:223406780-223407157	MCF10A-Er-Src	breast:	n/a	n/a
46	GABPA	chr1:223406756-223407152	K562	blood:	n/a	n/a
47	BHLHE40	chr1:223406749-223407743	K562	blood:	n/a	n/a
48	POLR2A	chr1:223406701-223407213	K562	blood:	n/a	n/a
49	JUN	chr1:223406791-223407665	K562	blood:	n/a	chr1:223407081-223407090 chr1:223407468-223407477 chr1:223407285-223407297
50	MYC	chr1:223406517-223407454	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:221914156..221916301-chr1:223405599..223408342,2	K562	blood:
2	chr1:223395360..223400819-chr1:223404357..223407646,5	K562	blood:
3	chr1:223405869..223408498-chr1:223417441..223419461,2	K562	blood:
4	chr1:223406203..223407902-chr1:225117204..225118811,2	K562	blood:
5	chr1:223400914..223405178-chr1:223405480..223408954,7	K562	blood:
6	chr1:223307471..223309121-chr1:223404472..223407072,2	MCF-7	breast:
7	chr1:223361935..223364100-chr1:223404912..223406820,2	K562	blood:
8	chr1:223398506..223401272-chr1:223405321..223406911,2	MCF-7	breast:
9	chr1:223406394..223408655-chr1:223414030..223416080,2	K562	blood:
10	chr1:223404846..223407473-chr1:223416172..223420942,6	K562	blood:
11	chr1:223364711..223366451-chr1:223405602..223407678,2	K562	blood:
12	chr1:223382567..223385980-chr1:223405719..223408418,3	K562	blood:

Variant related genes	Relation type
SUSD4	TF binding region
ENSG00000187554	Chromatin interaction
ENSG00000185842	Chromatin interaction
ENSG00000143507	Chromatin interaction
ENSG00000143502	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11485987	0.98[ASN][1000 genomes]
rs73120300	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs851140	1.00[ASN][1000 genomes]
rs851146	0.87[AMR][1000 genomes]
rs851209	0.91[ASN][1000 genomes]
rs851210	0.89[ASN][1000 genomes]
rs851211	0.91[ASN][1000 genomes]
rs851215	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223393200-223407800	Weak transcription	Brain Anterior Caudate	brain
2	chr1:223396600-223408200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:223400800-223408800	Enhancers	Fetal Thymus	thymus
4	chr1:223401800-223408400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:223401800-223408400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:223401800-223408400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr1:223402000-223408400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:223402200-223408400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:223402400-223407800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr1:223402400-223408400	Enhancers	Thymus	Thymus
11	chr1:223402600-223407600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:223402600-223408400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:223402800-223408400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:223402800-223408400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:223403000-223408000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:223404000-223408400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:223404200-223408200	Enhancers	HMEC	breast
18	chr1:223404200-223408400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr1:223404200-223408800	Enhancers	Primary T cells from cord blood	blood
20	chr1:223404400-223407000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:223404400-223408400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:223405400-223407400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:223405600-223408000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:223405600-223408200	Enhancers	HSMM	muscle
25	chr1:223405600-223408400	Enhancers	NH-A	brain
26	chr1:223405800-223408000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:223406000-223407800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:223406000-223407800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:223406000-223408000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:223406200-223407800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:223406200-223407800	Enhancers	Right Atrium	heart
32	chr1:223406200-223408000	Enhancers	Osteobl	bone
33	chr1:223406200-223408400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:223406400-223407600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:223406400-223407600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:223406400-223407600	Enhancers	HSMMtube	muscle
37	chr1:223406400-223407800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:223406400-223407800	Enhancers	Gastric	stomach
39	chr1:223406400-223407800	Enhancers	Stomach Mucosa	stomach
40	chr1:223406400-223407800	Enhancers	HUVEC	blood vessel
41	chr1:223406400-223407800	Enhancers	NHLF	lung
42	chr1:223406400-223408000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:223406400-223408000	Flanking Active TSS	K562	blood
44	chr1:223406600-223407000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:223406600-223407200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:223406600-223407400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr1:223406800-223407000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:223406800-223407000	Bivalent Enhancer	HepG2	liver
49	chr1:223406800-223407000	Flanking Active TSS	NHEK	skin
50	chr1:223406800-223407200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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